Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ph-d

Cell type

Cell type Class
Adult
Cell type
Ovary
NA
NA

Attributes by original data submitter

Sample

source_name
sorted germcell ChIPseq_FACS purified germ cell
uas-rnai
none
gal4/uas
nos-Gal4, UASp-NLS-GFP
developmental stage
bam ovary
tissue/cell type
FACS-purified germ cells
chip antibody
Ph (Buchenau et al., 1998)o (Brown et al., 2003)
spike-in normalization
none
library construction
DNA libraries prepared with Takara Bio ThruPLEX DNA seq

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
FACS-purified Drosophila melanogaster germ cells were mixed with either FACS purified Drosophila pseudoobscura follicle cells, mouse embryonic fibroblasts, or in some cases, no spike-in. Sequences were mapped to the D.mel6.02 genome or a hybrid genome of D.mel6.02/D.pse3.0 or D.mel /M.m10 and MAPQ 30 filtered. The ratio of Spike-in to D.mel reads was used to normalize enrichment between IP samples and normalized genome wide read coverage was calculated with Bedtools and supplied as a bigWig file for each sample. Normalized read depth was also was also calculated for overlapping 5kb bins annotated with a 3 or 4 state chromatin model and supplied as a modified bed file.

Sequencing Platform

instrument_model
NextSeq 500

dm6

Number of total reads
20054790
Reads aligned (%)
37.0
Duplicates removed (%)
34.7
Number of peaks
2062 (qval < 1E-05)

dm3

Number of total reads
20054790
Reads aligned (%)
37.6
Duplicates removed (%)
33.2
Number of peaks
658 (qval < 1E-05)

Base call quality data from DBCLS SRA